So, I recently got the Reference Rulebook and noticed that a new rule had been added for pre-game arming of heavy weapons.

Previously, a player could pre-load a multiple-turn arming heavy weapon (e.g. photorps), as long as the cost of pre-arming did not exceed batteries. Now the new rule states that this can only be done if all photorps on the ship pre-arm (this ruling also applies to other heavy weapons with multiple-turn arming sequences).

The problem is that I can't find a ship (of any race) that has enough battery power to pre-load all of its heavy weapons. What am I missing here?

The ship doesn't need to have enough batteries to pre-game arm, it just gives up all its battery power if it chooses to pre-game arm, but this battery power lost will not exceed the amount of power it took to pre-game arm.

So basically, if you pre-game arm, you start with empty batteries. It doesn't matter that your battery power would be insufficient to do the arming, the point it that the thing you give up if you pre-game arm is your battery power.

The only exception is the rare ship that has more than enough batteries to pre-game arm, and in that case they only start with empty batteries equal to what it would take to arm.